diff --git a/.changeset/moody-moose-fix.md b/.changeset/moody-moose-fix.md
new file mode 100644
index 0000000000..17aa6ef2c8
--- /dev/null
+++ b/.changeset/moody-moose-fix.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/headless": patch
+---
+
+Fixed a performance regression that was caused by [#3032](https://github.com/pnpm/pnpm/pull/3032).
diff --git a/packages/headless/src/index.ts b/packages/headless/src/index.ts
index 4f59a1ec09..7f6397101e 100644
--- a/packages/headless/src/index.ts
+++ b/packages/headless/src/index.ts
@@ -223,11 +223,6 @@ export default async (opts: HeadlessOptions) => {
       pnpmVersion: opts.currentEngine.pnpmVersion,
     } as LockfileToDepGraphOptions
   )
-  if (filteredLockfile.packages) {
-    for (const skippedDepPath of Array.from(skipped)) {
-      delete filteredLockfile.packages[skippedDepPath]
-    }
-  }
   if (opts.enablePnp) {
     const importerNames = R.fromPairs(
       opts.projects.map(({ manifest, id }) => [id, manifest.name ?? id])
@@ -276,8 +271,15 @@ export default async (opts: HeadlessOptions) => {
 
     let newHoistedDependencies!: HoistedDependencies
     if (opts.hoistPattern != null || opts.publicHoistPattern != null) {
+      // It is important to keep the skipped packages in the lockfile which will be saved as the "current lockfile".
+      // pnpm is comparing the current lockfile to the wanted one and they should much.
+      // But for hoisting, we need a version of the lockfile w/o the skipped packages, so we're making a copy.
+      const hoistLockfile = {
+        ...filteredLockfile,
+        packages: R.omit(Array.from(skipped), filteredLockfile.packages),
+      }
       newHoistedDependencies = await hoist({
-        lockfile: filteredLockfile,
+        lockfile: hoistLockfile,
         lockfileDir,
         privateHoistedModulesDir: hoistedModulesDir,
         privateHoistPattern: opts.hoistPattern ?? [],
diff --git a/packages/supi/test/install/hoist.ts b/packages/supi/test/install/hoist.ts
index 649e0b7cfe..90fdb89b00 100644
--- a/packages/supi/test/install/hoist.ts
+++ b/packages/supi/test/install/hoist.ts
@@ -502,7 +502,6 @@ test('should recreate node_modules with hoisting', async () => {
 
 test('hoisting should not create a broken symlink to a skipped optional dependency', async () => {
   const project = prepareEmpty()
-  console.log(process.cwd())
 
   await install({
     optionalDependencies: {
@@ -522,4 +521,9 @@ test('hoisting should not create a broken symlink to a skipped optional dependen
   }, await testDefaults({ publicHoistPattern: '*' }))
 
   await project.hasNot('dep-of-optional-pkg')
+
+  const rootModules = assertProject(process.cwd())
+  const currentLockfile = await rootModules.readCurrentLockfile()
+  const wantedLockfile = await rootModules.readLockfile()
+  expect(currentLockfile).toStrictEqual(wantedLockfile)
 })
\ No newline at end of file